Beta-aspartic acid (b-Asp) and gamma-glutamic acid (g-Glu) residues are amino acid residues in which the peptide bond is formed through the carboxylic acid group on the side chain rather than at the alpha carbon (normal). The form of aspartic acid (normal-Asp vs. b-Asp) in a peptide can greatly affect the activity of the peptide; likewise, the form of glutamic acid (normal-Glu vs. G-Glu) affects the peptide activity. We can identify the type of aspartic acid or glutamic acid linkage present by using analysis by MALDI-PSD of the TMPP-Ac-derivatives. The mass spectrum of the peptide containing a side chain-linked residue (b-Asp or g-Glu) had a b-type ion peak that was more intense than the corresponding b-type ion peak in the spectrum of the peptide containing the normal residue (Asp or Glu). Experiments with paired isomers of model peptides are being studied in an effort to establish useful protocols for identification of unknowns.